Primary Fermenter is where you will actually ferment the beer in.
The secondary fermenter is also called a "Brite Tank". In most cases its purpose is to help further clear up the beer. More often than not, no fermentation actually happens in the secondary fermenter, unless you introduce another fermentable to the secondary (i.e. fruits).
People will argue the pros and cons of actually using a secondary fermenter, if you are a new brewer I suggest using one. By using a secondary you will rack your beer off of most of the trub from the primary. What little trub you did transfer over to the secondary will settle out and when you transfer your beer to your bottling bucket you will move over even less of it. While your beer is settling in the secondary, you can make another brew and put it into the primary. Pipeline!